Fix unused variable warnings

ebwt.h

@@ -487,7 +487,7 @@ class Ebwt {
 	         isaRate,
 	         ftabChars,
 	         refparams.reverse == REF_READ_REVERSE,
-	         false /* is this a bt2 index? */)
+	         isBt2Index)
 	{
 		_packed = packed;
 	 #ifdef POPCNT_CAPABILITY

ebwt_search.cpp

@@ -1381,7 +1381,7 @@ static void exactSearch(PatternComposer& _patsrc,
 		for(int i = 0; i < nthreads; i++) {
 			tids[i] = i;
 #if (__cplusplus >= 201103L)
-			tps[i].tid = i;
+			tps[i].tid = tids[i];
 			tps[i].done = &all_threads_done;
 			if (i == nthreads - 1) {
 				if(stateful) {
@@ -1762,7 +1762,7 @@ static void mismatchSearchFull(PatternComposer& _patsrc,
 		for(int i = 0; i < nthreads; i++) {
 			tids[i] = i;
 #if (__cplusplus >= 201103L)
-			tps[i].tid = i;
+			tps[i].tid = tids[i];
 			tps[i].done = &all_threads_done;
 			if (i == nthreads - 1) {
 				if(stateful) {
@@ -2258,7 +2258,7 @@ static void twoOrThreeMismatchSearchFull(
 		for(int i = 0; i < nthreads; i++) {
 			tids[i] = i;
 #if (__cplusplus >= 201103L)
-			tps[i].tid = i;
+			tps[i].tid = tids[i];
 			tps[i].done = &all_threads_done;
 			if (i == nthreads - 1) {
 				if(stateful) {
@@ -2804,7 +2804,7 @@ static void seededQualCutoffSearchFull(
 		for(int i = 0; i < nthreads; i++) {
 			tids[i] = i;
 #if (__cplusplus >= 201103L)
-			tps[i].tid = i;
+			tps[i].tid = tids[i];
 			tps[i].done = &all_threads_done;
 			if (i == nthreads - 1) {
 				if(stateful) {
@@ -2920,9 +2920,7 @@ patsrcFromStrings(int format,
 	switch(format) {
 		case FASTA:
 			return new FastaPatternSource (reads, quals,
-			                               trim3, trim5,
-			                               solexaQuals, phred64Quals,
-			                               integerQuals);
+			                               trim3, trim5);
 		case FASTA_CONT:
 			return new FastaContinuousPatternSource (
 			                               reads, fastaContLen,

pat.h

@@ -464,19 +464,13 @@ class FastaPatternSource : public CFilePatternSource {
 		const EList<string>& infiles,
 		const EList<string>* qinfiles,
 		int trim3 = 0,
-		int trim5 = 0,
-		bool solexa64 = false,
-		bool phred64 = false,
-		bool intQuals = false) :
+		int trim5 = 0) :
 		CFilePatternSource(
 			infiles,
 			qinfiles,
 			trim3,
 			trim5),
-		first_(true),
-		solexa64_(solexa64),
-		phred64_(phred64),
-		intQuals_(intQuals) { }
+		first_(true) { }
 
 	/**
 	 * Reset so that next call to nextBatch* gets the first batch.
@@ -520,9 +514,6 @@ class FastaPatternSource : public CFilePatternSource {
 private:
 
 	bool first_;
-	bool solexa64_;
-	bool phred64_;
-	bool intQuals_;
 };
 
 

range_cache.h

@@ -179,7 +179,8 @@ class RangeCacheEntry {
 			// Get the pointer to the entries themselves
 			ents_ = ents + 1;
 		}
-		assert(sanityCheckEnts());
+		if (sanity_)
+			assert(sanityCheckEnts());
 	}
 
 	/**
@@ -203,7 +204,8 @@ class RangeCacheEntry {
 		// Get the pointer to the entries themselves
 		ents_ = ents + 1;
 		assert_leq(top_ + len_, ebwt_->_eh._len);
-		assert(sanityCheckEnts());
+		if (sanity_)
+			assert(sanityCheckEnts());
 	}
 
 	TIndexOffU len() const   {
@@ -401,7 +403,8 @@ class RangeCache {
 			}
 			TIndexOffU len = ents[0];
 			assert_leq(top + len, ebwt_->_eh._len);
-			RangeCacheEntry::sanityCheckEnts(len, ents + 1, ebwt_);
+			if (sanity_)
+				RangeCacheEntry::sanityCheckEnts(len, ents + 1, ebwt_);
 		}
 #endif
 		return true;

read.h

@@ -59,7 +59,6 @@ struct Read {
 		patRcRev.clear();
 		qualRev.clear();
 		name.clear();
-		preservedOptFlags.clear();
 		filter = '?';
 		seed = 0;
 		parsed = false;
@@ -259,7 +258,6 @@ struct Read {
 	TBuf readOrigBuf;
 
 	BTString name;      // read name
-	BTString preservedOptFlags;
 	TReadId  rdid;      // 0-based id based on pair's offset in read file(s)
 	int      mate;      // 0 = single-end, 1 = mate1, 2 = mate2
 	uint32_t seed;      // random seed